Primer (molecular biology)
Short nucleic acid used to start DNA replication.
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DNA polymerases can only add nucleotides to an existing 3'-end, so a primer must be bound to the template before a complementary strand can be built.[1] Synthetic primers are chemically synthesized oligonucleotides that can be customized to anneal to a specific DNA site.[1]
Quick Facts
- Field
- Molecular biology
- Known for
- Initiation of DNA synthesis
Facts from the source article.
Key facts and history
Living organisms use RNA primers to start DNA strand synthesis, added de novo by enzymes called primases.[1] On the leading strand, a single RNA primer initiates continuous DNA synthesis moving with the replication fork.[1] On the lagging strand, the template runs 5′→3′, so DNA is synthesized backward in short Okazaki fragments requiring multiple RNA primers.[1] The long flap pathway uses Pif1 helicase to elongate the flap, which is then cleaved by DNA2 nuclease and FEN1.[2]
Reverse transcriptase also requires an existing 3' end to synthesize DNA from an RNA template.[1] PCR uses a pair of custom primers, typically 18–24 bases long, to direct DNA elongation toward each other.[1] Following the insertion of Okazaki fragments, the RNA primers are taken out and deoxyribonucleotides are put in their place.[1] In prokaryotes, DNA polymerase I performs nick translation, where it concurrently removes primer ribonucleotides and adds deoxyribonucleotides.[1]
To prevent non-specific structures that lower reaction efficiency, primer pairs are given similar melting temperatures.[3]
What the research sources say
Additional nucleotide bases can be added to primer ends for applications such as TA cloning, where AG tails improve efficiency.[4] Primer-BLAST, a free tool from NCBI, combines primer design with a BLAST search to assist in choosing unique primer sequences.[5][6] To avoid loop formation and mishybridization, primer sequences ought to steer clear of areas with many mononucleotide and dinucleotide repeats.[7][8]
References
- Wikipedia, "Primer (molecular biology)" (CC BY-SA 4.0), which cites: "Molecular Biology: Principles and practice", W. H. Freeman, December 21, 2016 (we also read that source) en.wikipedia.org
- Wikipedia, "Primer (molecular biology)" (CC BY-SA 4.0), which cites: Uhler, "Primer removal during mammalian mitochondrial DNA replication", DNA Repair, 2015-10-01, p. 28–38 (original not read by us) en.wikipedia.org
- Wikipedia, "Primer (molecular biology)" (CC BY-SA 4.0), which cites: Bakhtiarizadeh, "Versatility of different melting temperature (Tm) calculator software for robust PCR and real-time PCR oligonucleotide design: A practical guide", Gene Reports, March 2016, p. 1–3 (original not read by us) en.wikipedia.org
- Wikipedia, "Primer (molecular biology)" (CC BY-SA 4.0), which cites: Peng, "Adenosine added on the primer 5′ end improved TA cloning efficiency of polymerase chain reaction products", Analytical Biochemistry, April 2007, p. 163–165 (original not read by us) en.wikipedia.org
- "Primer-BLAST", NCBI. facts only, no text reused. ncbi.nlm.nih.gov
- Wikipedia, "Primer (molecular biology)" (CC BY-SA 4.0), which cites: "Primer-BLAST", NCBI (we also read that source) en.wikipedia.org
- Open Library record, ISBN 9781402062414 ("Principles and technical aspects of PCR amplification"). CC0 (metadata); book content not read. openlibrary.org
- Wikipedia, "Primer (molecular biology)" (CC BY-SA 4.0), which cites: "Principles and Technical Aspects of PCR Amplification", Springer Netherlands, 2008, p. 63–90; "Principles and Technical Aspects of PCR Amplification", Springer Netherlands, 2008, p. 63–90 (we also read that source) en.wikipedia.org
Each numbered sentence above was checked against the source it cites before publication. Sentences citing Wikipedia adapt text from the English Wikipedia article Primer (molecular biology) (contributors), used under CC BY-SA 4.0; this entry is available under the same licence. Other sources were used for facts only; no text or images are copied from them.
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Sources
Compiled from Wikipedia and the sources listed below. Text from Wikipedia is available under CC BY-SA 4.0; this entry is adapted from it.
- Wikipedia: Primer (molecular biology) (CC BY-SA 4.0).
- Word definitions: the , each quoted from its Wikipedia article.
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